There is a workaround for this: add 2 outputs with fixed value lines, and then don't display them. This way two copies of the same indicator with different will stay aligned.
example:
outputParameterInfos = new OutputParameterInfo[]
{
new OutputParameterInfo("CCI", OutputParameterInfo.Type.DOUBLE, OutputParameterInfo.DrawingStyle.LINE),
new OutputParameterInfo("Upper Level", OutputParameterInfo.Type.DOUBLE, OutputParameterInfo.DrawingStyle.DASH_LINE),
new OutputParameterInfo("Lower Level", OutputParameterInfo.Type.DOUBLE, OutputParameterInfo.DrawingStyle.DASH_LINE)
};
outputParameterInfos[1].setShowOutput(false);
outputParameterInfos[2].setShowOutput(false);
if the upper and lower levels are set to sufficiently large values, the actual indicator values won't exceed them so 2 copies of the indicator in the same pane will stay aligned.